The healer I have the most experience with is WHM, so I'm more comfortable trying to put out ideas to fix it than others...

One change for all would be to make their DoT into an AoE for the sake of dungeons... But, aside from that for WHM

Keep Stone I to Stone IV as the primary attack spell, and just increase their potency through traits throughout the levels.
Make Glare I to Glare IV into a separate spell, one that requires stacks of Sacred Sight to cast as the way Glare IV currently does.
Entirely replace Freecure with a new trait with one that would grant a stack of Sacred Sight at about 30% proc chance on ever Spell cast.
Replace Planary Indulgence with Seraph Strike, make Seraph Strike cost 1 Lily to use and nourish the Blood Lily.
Because of a better alternative for nourishing the Blood Lily, Afflatus Misery's potency can be dropped as it no longer would have to be DPS neutral to Glare(or Stone with these changes).
Remove MP recovery from Assize, and add it to Afflatus Solace and Afflatus Rapture.